Multiple sequence alignment - TraesCS4D01G183100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G183100 chr4D 100.000 4428 0 0 1 4428 320211692 320207265 0.000000e+00 8178.0
1 TraesCS4D01G183100 chr4B 96.238 1781 32 8 1021 2784 400399476 400401238 0.000000e+00 2885.0
2 TraesCS4D01G183100 chr4B 94.863 876 29 6 2790 3649 400401389 400402264 0.000000e+00 1354.0
3 TraesCS4D01G183100 chr4B 88.889 630 28 24 1 613 400398501 400399105 0.000000e+00 737.0
4 TraesCS4D01G183100 chr4B 93.407 182 11 1 655 836 400399112 400399292 7.300000e-68 268.0
5 TraesCS4D01G183100 chr4B 94.521 73 4 0 921 993 400399308 400399380 3.620000e-21 113.0
6 TraesCS4D01G183100 chr4A 96.214 1479 41 5 2788 4254 152740546 152742021 0.000000e+00 2407.0
7 TraesCS4D01G183100 chr4A 95.534 1433 34 8 1021 2439 152738589 152740005 0.000000e+00 2265.0
8 TraesCS4D01G183100 chr4A 89.799 647 31 17 1 620 152651309 152651947 0.000000e+00 797.0
9 TraesCS4D01G183100 chr4A 95.614 342 13 2 2444 2784 152740057 152740397 8.370000e-152 547.0
10 TraesCS4D01G183100 chr4A 87.864 206 7 4 814 1019 152734502 152734689 4.460000e-55 226.0
11 TraesCS4D01G183100 chr4A 97.849 93 2 0 4261 4353 152744752 152744844 1.270000e-35 161.0
12 TraesCS4D01G183100 chr1B 92.405 474 18 10 1 459 638035762 638036232 0.000000e+00 660.0
13 TraesCS4D01G183100 chr1B 94.286 70 4 0 541 610 638043174 638043243 1.680000e-19 108.0
14 TraesCS4D01G183100 chr2B 100.000 46 0 0 611 656 678369896 678369851 7.890000e-13 86.1
15 TraesCS4D01G183100 chr2B 82.278 79 10 4 305 381 28325209 28325285 1.030000e-06 65.8
16 TraesCS4D01G183100 chr2D 85.246 61 7 2 322 381 16058471 16058530 1.330000e-05 62.1
17 TraesCS4D01G183100 chr2A 80.769 78 13 2 305 381 17956215 17956291 4.780000e-05 60.2
18 TraesCS4D01G183100 chr2A 84.746 59 7 2 324 381 17988660 17988717 1.720000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G183100 chr4D 320207265 320211692 4427 True 8178.0 8178 100.0000 1 4428 1 chr4D.!!$R1 4427
1 TraesCS4D01G183100 chr4B 400398501 400402264 3763 False 1071.4 2885 93.5836 1 3649 5 chr4B.!!$F1 3648
2 TraesCS4D01G183100 chr4A 152734502 152744844 10342 False 1121.2 2407 94.6150 814 4353 5 chr4A.!!$F2 3539
3 TraesCS4D01G183100 chr4A 152651309 152651947 638 False 797.0 797 89.7990 1 620 1 chr4A.!!$F1 619

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
653 691 0.106419 TTGCCCCTTGGTCTCGTTTT 60.106 50.000 0.00 0.0 0.0 2.43 F
1041 5017 0.391228 TTCAGTTCGGTGCAGCACTA 59.609 50.000 24.75 11.0 34.4 2.74 F
2297 6289 2.095853 AGGTGCGAATTTATGAAGTGCG 59.904 45.455 0.00 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2546 6585 2.699251 CCAACAAGGGCTACGAAAAC 57.301 50.000 0.00 0.00 0.00 2.43 R
2785 6829 4.881850 CGGAAGTACCCTTGATGCTATTTT 59.118 41.667 0.00 0.00 34.64 1.82 R
4077 8290 0.674895 CCTCCCGCAAGCTATATGGC 60.675 60.000 2.23 2.23 0.00 4.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 144 2.498481 GCACGGTACCATAGCCCATATA 59.502 50.000 13.54 0.00 0.00 0.86
139 145 3.134081 GCACGGTACCATAGCCCATATAT 59.866 47.826 13.54 0.00 0.00 0.86
140 146 4.342951 GCACGGTACCATAGCCCATATATA 59.657 45.833 13.54 0.00 0.00 0.86
141 147 5.509163 GCACGGTACCATAGCCCATATATAG 60.509 48.000 13.54 0.00 0.00 1.31
195 220 5.581085 GGAGTTTATATGTGACTCAGCGTTT 59.419 40.000 13.50 0.00 41.15 3.60
210 235 1.662360 CGTTTGCGTTGATCTGTGTG 58.338 50.000 0.00 0.00 0.00 3.82
212 237 2.219903 CGTTTGCGTTGATCTGTGTGTA 59.780 45.455 0.00 0.00 0.00 2.90
213 238 3.120683 CGTTTGCGTTGATCTGTGTGTAT 60.121 43.478 0.00 0.00 0.00 2.29
214 239 4.610456 CGTTTGCGTTGATCTGTGTGTATT 60.610 41.667 0.00 0.00 0.00 1.89
340 365 1.735559 GTACGTGTTCTGGGACGCC 60.736 63.158 0.00 0.00 39.22 5.68
470 495 5.050295 GCTTAGCTTGGAACCAATCGTATAC 60.050 44.000 6.74 0.00 35.20 1.47
472 497 5.864418 AGCTTGGAACCAATCGTATACTA 57.136 39.130 6.74 0.00 35.20 1.82
499 537 3.930336 TGTATCTCAGAGGCTGTTGTTG 58.070 45.455 0.00 0.00 32.61 3.33
500 538 3.324846 TGTATCTCAGAGGCTGTTGTTGT 59.675 43.478 0.00 0.00 32.61 3.32
501 539 3.498774 ATCTCAGAGGCTGTTGTTGTT 57.501 42.857 0.00 0.00 32.61 2.83
504 542 0.954452 CAGAGGCTGTTGTTGTTCCC 59.046 55.000 0.00 0.00 0.00 3.97
507 545 0.846693 AGGCTGTTGTTGTTCCCTCT 59.153 50.000 0.00 0.00 0.00 3.69
512 550 3.480470 CTGTTGTTGTTCCCTCTGTGAT 58.520 45.455 0.00 0.00 0.00 3.06
520 558 1.815421 CCCTCTGTGATTTCCCGCG 60.815 63.158 0.00 0.00 0.00 6.46
529 567 2.515996 GATTTCCCGCGGAGTGTCCA 62.516 60.000 30.73 2.84 35.91 4.02
530 568 2.521958 ATTTCCCGCGGAGTGTCCAG 62.522 60.000 30.73 7.15 35.91 3.86
533 571 3.449227 CCGCGGAGTGTCCAGCTA 61.449 66.667 24.07 0.00 35.91 3.32
534 572 2.103143 CGCGGAGTGTCCAGCTAG 59.897 66.667 0.00 0.00 35.91 3.42
535 573 2.496817 GCGGAGTGTCCAGCTAGG 59.503 66.667 0.00 0.00 35.91 3.02
536 574 2.352032 GCGGAGTGTCCAGCTAGGT 61.352 63.158 0.00 0.00 35.91 3.08
537 575 1.035932 GCGGAGTGTCCAGCTAGGTA 61.036 60.000 0.00 0.00 35.91 3.08
538 576 0.739561 CGGAGTGTCCAGCTAGGTAC 59.260 60.000 0.00 0.00 35.91 3.34
615 653 3.551846 TCATCTGCGAGGTGTGTCTATA 58.448 45.455 0.00 0.00 0.00 1.31
616 654 3.951680 TCATCTGCGAGGTGTGTCTATAA 59.048 43.478 0.00 0.00 0.00 0.98
618 656 4.794278 TCTGCGAGGTGTGTCTATAAAA 57.206 40.909 0.00 0.00 0.00 1.52
619 657 5.142061 TCTGCGAGGTGTGTCTATAAAAA 57.858 39.130 0.00 0.00 0.00 1.94
620 658 5.730550 TCTGCGAGGTGTGTCTATAAAAAT 58.269 37.500 0.00 0.00 0.00 1.82
621 659 6.869695 TCTGCGAGGTGTGTCTATAAAAATA 58.130 36.000 0.00 0.00 0.00 1.40
622 660 7.497595 TCTGCGAGGTGTGTCTATAAAAATAT 58.502 34.615 0.00 0.00 0.00 1.28
623 661 7.438160 TCTGCGAGGTGTGTCTATAAAAATATG 59.562 37.037 0.00 0.00 0.00 1.78
624 662 6.018262 TGCGAGGTGTGTCTATAAAAATATGC 60.018 38.462 0.00 0.00 0.00 3.14
625 663 6.565999 GCGAGGTGTGTCTATAAAAATATGCC 60.566 42.308 0.00 0.00 0.00 4.40
626 664 6.346598 CGAGGTGTGTCTATAAAAATATGCCG 60.347 42.308 0.00 0.00 0.00 5.69
627 665 5.763204 AGGTGTGTCTATAAAAATATGCCGG 59.237 40.000 0.00 0.00 0.00 6.13
628 666 5.048991 GGTGTGTCTATAAAAATATGCCGGG 60.049 44.000 2.18 0.00 0.00 5.73
629 667 5.048991 GTGTGTCTATAAAAATATGCCGGGG 60.049 44.000 2.18 0.00 0.00 5.73
630 668 4.457949 GTGTCTATAAAAATATGCCGGGGG 59.542 45.833 2.18 0.00 0.00 5.40
631 669 4.105057 TGTCTATAAAAATATGCCGGGGGT 59.895 41.667 2.18 0.00 0.00 4.95
632 670 4.457949 GTCTATAAAAATATGCCGGGGGTG 59.542 45.833 2.18 0.00 0.00 4.61
633 671 1.404843 TAAAAATATGCCGGGGGTGC 58.595 50.000 2.18 0.00 0.00 5.01
634 672 0.325203 AAAAATATGCCGGGGGTGCT 60.325 50.000 2.18 0.00 0.00 4.40
635 673 0.325203 AAAATATGCCGGGGGTGCTT 60.325 50.000 2.18 0.00 0.00 3.91
636 674 1.042559 AAATATGCCGGGGGTGCTTG 61.043 55.000 2.18 0.00 0.00 4.01
637 675 4.813235 TATGCCGGGGGTGCTTGC 62.813 66.667 2.18 0.00 0.00 4.01
645 683 4.621087 GGGTGCTTGCCCCTTGGT 62.621 66.667 10.55 0.00 42.89 3.67
646 684 2.991540 GGTGCTTGCCCCTTGGTC 60.992 66.667 0.00 0.00 0.00 4.02
647 685 2.116125 GTGCTTGCCCCTTGGTCT 59.884 61.111 0.00 0.00 0.00 3.85
648 686 1.973812 GTGCTTGCCCCTTGGTCTC 60.974 63.158 0.00 0.00 0.00 3.36
649 687 2.747855 GCTTGCCCCTTGGTCTCG 60.748 66.667 0.00 0.00 0.00 4.04
650 688 2.750350 CTTGCCCCTTGGTCTCGT 59.250 61.111 0.00 0.00 0.00 4.18
651 689 1.073199 CTTGCCCCTTGGTCTCGTT 59.927 57.895 0.00 0.00 0.00 3.85
652 690 0.537371 CTTGCCCCTTGGTCTCGTTT 60.537 55.000 0.00 0.00 0.00 3.60
653 691 0.106419 TTGCCCCTTGGTCTCGTTTT 60.106 50.000 0.00 0.00 0.00 2.43
719 757 5.445806 CGTTGATGATTGCAGTATTGTCGAA 60.446 40.000 0.00 0.00 0.00 3.71
725 763 4.725556 TTGCAGTATTGTCGAACTCAAC 57.274 40.909 0.00 0.00 0.00 3.18
738 776 4.035909 TCGAACTCAACGGATAATCGATCA 59.964 41.667 0.00 0.00 36.12 2.92
748 786 2.485266 TAATCGATCACGTGCGACAT 57.515 45.000 18.34 13.35 39.56 3.06
758 796 2.860136 CACGTGCGACATATTGTGATCT 59.140 45.455 0.82 0.00 0.00 2.75
761 799 3.060940 CGTGCGACATATTGTGATCTGAC 60.061 47.826 0.00 0.00 0.00 3.51
807 845 1.433879 CGGCGTTTCCAACCAAACA 59.566 52.632 0.00 0.00 36.23 2.83
812 850 2.601314 GCGTTTCCAACCAAACAGAAAC 59.399 45.455 0.00 0.00 42.87 2.78
836 874 8.371770 ACTGCAGTTCTTTTTGTTTTGTTTTA 57.628 26.923 15.25 0.00 0.00 1.52
837 875 8.998377 ACTGCAGTTCTTTTTGTTTTGTTTTAT 58.002 25.926 15.25 0.00 0.00 1.40
838 876 9.824534 CTGCAGTTCTTTTTGTTTTGTTTTATT 57.175 25.926 5.25 0.00 0.00 1.40
901 939 4.024048 AGAGTAGCCGTTGATGTTTTTGTG 60.024 41.667 0.00 0.00 0.00 3.33
903 941 3.518634 AGCCGTTGATGTTTTTGTGTT 57.481 38.095 0.00 0.00 0.00 3.32
904 942 3.855858 AGCCGTTGATGTTTTTGTGTTT 58.144 36.364 0.00 0.00 0.00 2.83
905 943 4.249661 AGCCGTTGATGTTTTTGTGTTTT 58.750 34.783 0.00 0.00 0.00 2.43
906 944 4.092675 AGCCGTTGATGTTTTTGTGTTTTG 59.907 37.500 0.00 0.00 0.00 2.44
907 945 4.143009 GCCGTTGATGTTTTTGTGTTTTGT 60.143 37.500 0.00 0.00 0.00 2.83
908 946 5.062308 GCCGTTGATGTTTTTGTGTTTTGTA 59.938 36.000 0.00 0.00 0.00 2.41
909 947 6.462647 CCGTTGATGTTTTTGTGTTTTGTAC 58.537 36.000 0.00 0.00 0.00 2.90
910 948 6.309251 CCGTTGATGTTTTTGTGTTTTGTACT 59.691 34.615 0.00 0.00 0.00 2.73
911 949 7.485277 CCGTTGATGTTTTTGTGTTTTGTACTA 59.515 33.333 0.00 0.00 0.00 1.82
912 950 8.308320 CGTTGATGTTTTTGTGTTTTGTACTAC 58.692 33.333 0.00 0.00 0.00 2.73
913 951 9.349145 GTTGATGTTTTTGTGTTTTGTACTACT 57.651 29.630 0.00 0.00 0.00 2.57
914 952 8.903570 TGATGTTTTTGTGTTTTGTACTACTG 57.096 30.769 0.00 0.00 0.00 2.74
915 953 8.516234 TGATGTTTTTGTGTTTTGTACTACTGT 58.484 29.630 0.00 0.00 0.00 3.55
916 954 9.991388 GATGTTTTTGTGTTTTGTACTACTGTA 57.009 29.630 0.00 0.00 0.00 2.74
1013 1091 4.217754 TCCGGAGAAAACAAAAACATCG 57.782 40.909 0.00 0.00 0.00 3.84
1019 1097 7.075741 CGGAGAAAACAAAAACATCGAAGTAT 58.924 34.615 0.00 0.00 0.00 2.12
1041 5017 0.391228 TTCAGTTCGGTGCAGCACTA 59.609 50.000 24.75 11.00 34.40 2.74
1065 5043 9.947669 CTACGCAATTTAGAGTAGTACTGTATT 57.052 33.333 7.76 0.00 37.20 1.89
1674 5653 4.511826 GGTCGTCAATCTGTTCAGTTTCTT 59.488 41.667 0.00 0.00 0.00 2.52
1675 5654 5.007724 GGTCGTCAATCTGTTCAGTTTCTTT 59.992 40.000 0.00 0.00 0.00 2.52
1676 5655 6.130058 GTCGTCAATCTGTTCAGTTTCTTTC 58.870 40.000 0.00 0.00 0.00 2.62
1677 5656 6.018669 GTCGTCAATCTGTTCAGTTTCTTTCT 60.019 38.462 0.00 0.00 0.00 2.52
1692 5671 7.273815 CAGTTTCTTTCTCAGTAGACGGTAATC 59.726 40.741 0.00 0.00 0.00 1.75
1779 5770 3.054878 GCAGAGCAAATGAAACACAAGG 58.945 45.455 0.00 0.00 0.00 3.61
1782 5773 4.741676 CAGAGCAAATGAAACACAAGGTTC 59.258 41.667 0.00 0.00 39.29 3.62
1834 5826 8.990163 TTCAGTATGGGGAAATTTTATACTCC 57.010 34.615 11.89 2.32 33.57 3.85
1835 5827 8.344939 TCAGTATGGGGAAATTTTATACTCCT 57.655 34.615 11.89 0.00 33.57 3.69
1836 5828 9.455144 TCAGTATGGGGAAATTTTATACTCCTA 57.545 33.333 11.89 0.00 33.57 2.94
1837 5829 9.503399 CAGTATGGGGAAATTTTATACTCCTAC 57.497 37.037 11.89 5.75 33.57 3.18
1972 5964 4.848299 GCTTTGCTTGTTGTCTTCTAATCG 59.152 41.667 0.00 0.00 0.00 3.34
1982 5974 3.007506 TGTCTTCTAATCGGCCTTTGTCA 59.992 43.478 0.00 0.00 0.00 3.58
2297 6289 2.095853 AGGTGCGAATTTATGAAGTGCG 59.904 45.455 0.00 0.00 0.00 5.34
2346 6338 9.128107 CTTAACTTACAGCCAATATTTGTTGTG 57.872 33.333 16.22 6.00 31.69 3.33
2348 6340 7.753309 ACTTACAGCCAATATTTGTTGTGTA 57.247 32.000 16.22 6.79 31.69 2.90
2434 6426 5.462068 GTGTTAATGAAAAACCAGGCAGAAC 59.538 40.000 0.00 0.00 0.00 3.01
2454 6493 7.413438 GCAGAACTAGATTGATTTGGTACACTG 60.413 40.741 0.00 0.00 39.29 3.66
2546 6585 7.029563 GCATTCTAGTTAATTTGTGTTCCTGG 58.970 38.462 0.00 0.00 0.00 4.45
2551 6590 8.626526 TCTAGTTAATTTGTGTTCCTGGTTTTC 58.373 33.333 0.00 0.00 0.00 2.29
2775 6819 6.235231 TCACAAAGGACACTAGAAGTCTTT 57.765 37.500 15.91 13.04 36.95 2.52
2784 6828 6.590677 GGACACTAGAAGTCTTTGGTCAATAC 59.409 42.308 15.91 0.00 36.29 1.89
2785 6829 7.062749 ACACTAGAAGTCTTTGGTCAATACA 57.937 36.000 0.00 0.00 0.00 2.29
2972 7163 7.560991 TGTCATATGGGCACTAAGATGAATTTT 59.439 33.333 2.13 0.00 28.28 1.82
2974 7165 8.415553 TCATATGGGCACTAAGATGAATTTTTG 58.584 33.333 2.13 0.00 0.00 2.44
3040 7231 4.265073 TCTCTTTAGCAATCCCAGCTTTC 58.735 43.478 0.00 0.00 43.25 2.62
3061 7252 7.572168 GCTTTCTTTTGTGCAAACTTTTAACCA 60.572 33.333 0.00 0.00 0.00 3.67
3657 7862 3.953612 TGAAGAAACTGCCATGTTGTTCT 59.046 39.130 0.00 0.00 30.90 3.01
3681 7886 6.223120 TGAAGAAATCGTCATCTCTTCACAA 58.777 36.000 8.82 0.00 45.43 3.33
3687 7892 6.952935 ATCGTCATCTCTTCACAACTAAAC 57.047 37.500 0.00 0.00 0.00 2.01
3698 7903 4.695396 TCACAACTAAACTACCAGCGAAA 58.305 39.130 0.00 0.00 0.00 3.46
3717 7922 6.797033 AGCGAAATTGTTCAAAATAGAGAACG 59.203 34.615 0.00 0.00 45.34 3.95
3724 7929 3.655486 TCAAAATAGAGAACGTTCGCCA 58.345 40.909 25.54 15.07 0.00 5.69
3857 8070 1.370778 CACCGTCACGTCGCAACTA 60.371 57.895 0.00 0.00 0.00 2.24
3930 8143 9.141400 AGAGAATGTTCGTCAGTTAGTATTTTC 57.859 33.333 0.00 0.00 0.00 2.29
3971 8184 4.141344 ACGGCTTATATGGTATGTTTGGGT 60.141 41.667 0.00 0.00 0.00 4.51
3998 8211 7.396907 TGGTAAGGATTGACATCACATTTCATT 59.603 33.333 0.00 0.00 0.00 2.57
4077 8290 1.106285 GGCCTATGCTTGGTTTGGAG 58.894 55.000 0.00 0.00 37.74 3.86
4236 8449 3.977134 AGACATTGCATGTGAGACTCT 57.023 42.857 3.68 0.00 45.03 3.24
4254 8467 6.344500 AGACTCTGTCCATACAAATTGCTAG 58.656 40.000 0.00 0.00 34.49 3.42
4346 11283 1.935873 TCAGCATGCTATTCAACGCTC 59.064 47.619 22.19 0.00 35.93 5.03
4353 11290 2.758423 TGCTATTCAACGCTCCACTAGA 59.242 45.455 0.00 0.00 0.00 2.43
4354 11291 3.181486 TGCTATTCAACGCTCCACTAGAG 60.181 47.826 0.00 0.00 46.29 2.43
4361 11298 2.811101 CTCCACTAGAGCAGCCCG 59.189 66.667 0.00 0.00 35.31 6.13
4362 11299 2.037367 TCCACTAGAGCAGCCCGT 59.963 61.111 0.00 0.00 0.00 5.28
4363 11300 2.185350 CCACTAGAGCAGCCCGTG 59.815 66.667 0.00 0.00 0.00 4.94
4364 11301 2.650116 CCACTAGAGCAGCCCGTGT 61.650 63.158 0.00 0.00 0.00 4.49
4365 11302 1.293498 CACTAGAGCAGCCCGTGTT 59.707 57.895 0.00 0.00 0.00 3.32
4366 11303 0.737715 CACTAGAGCAGCCCGTGTTC 60.738 60.000 0.00 0.00 36.66 3.18
4367 11304 1.153549 CTAGAGCAGCCCGTGTTCC 60.154 63.158 0.00 0.00 37.09 3.62
4368 11305 2.890847 CTAGAGCAGCCCGTGTTCCG 62.891 65.000 0.00 0.00 37.09 4.30
4379 11316 2.044888 CGTGTTCCGGTGAAAATTGG 57.955 50.000 0.00 0.00 30.79 3.16
4380 11317 1.604755 CGTGTTCCGGTGAAAATTGGA 59.395 47.619 0.00 0.00 30.79 3.53
4381 11318 2.603652 CGTGTTCCGGTGAAAATTGGAC 60.604 50.000 0.00 0.00 30.79 4.02
4382 11319 1.604755 TGTTCCGGTGAAAATTGGACG 59.395 47.619 0.00 0.00 30.79 4.79
4383 11320 1.068816 GTTCCGGTGAAAATTGGACGG 60.069 52.381 0.00 0.00 42.45 4.79
4384 11321 0.606944 TCCGGTGAAAATTGGACGGG 60.607 55.000 0.00 0.00 41.49 5.28
4385 11322 1.591504 CCGGTGAAAATTGGACGGGG 61.592 60.000 0.00 0.00 37.80 5.73
4386 11323 0.606944 CGGTGAAAATTGGACGGGGA 60.607 55.000 0.00 0.00 0.00 4.81
4387 11324 1.173913 GGTGAAAATTGGACGGGGAG 58.826 55.000 0.00 0.00 0.00 4.30
4388 11325 1.173913 GTGAAAATTGGACGGGGAGG 58.826 55.000 0.00 0.00 0.00 4.30
4389 11326 0.610785 TGAAAATTGGACGGGGAGGC 60.611 55.000 0.00 0.00 0.00 4.70
4390 11327 1.654023 GAAAATTGGACGGGGAGGCG 61.654 60.000 0.00 0.00 0.00 5.52
4391 11328 4.796495 AATTGGACGGGGAGGCGC 62.796 66.667 0.00 0.00 0.00 6.53
4396 11333 4.899239 GACGGGGAGGCGCATCAG 62.899 72.222 24.79 16.17 0.00 2.90
4398 11335 4.161295 CGGGGAGGCGCATCAGAA 62.161 66.667 24.79 0.00 0.00 3.02
4399 11336 2.514824 GGGGAGGCGCATCAGAAC 60.515 66.667 24.79 10.32 0.00 3.01
4400 11337 2.268920 GGGAGGCGCATCAGAACA 59.731 61.111 24.79 0.00 0.00 3.18
4401 11338 1.153086 GGGAGGCGCATCAGAACAT 60.153 57.895 24.79 0.00 0.00 2.71
4402 11339 1.442526 GGGAGGCGCATCAGAACATG 61.443 60.000 24.79 0.00 0.00 3.21
4403 11340 1.354506 GAGGCGCATCAGAACATGC 59.645 57.895 18.55 0.00 45.01 4.06
4423 11360 3.192466 GCATGATGCAAAATGAAGGACC 58.808 45.455 13.36 0.00 44.26 4.46
4424 11361 3.788937 CATGATGCAAAATGAAGGACCC 58.211 45.455 6.18 0.00 0.00 4.46
4425 11362 3.173953 TGATGCAAAATGAAGGACCCT 57.826 42.857 0.00 0.00 0.00 4.34
4426 11363 3.509442 TGATGCAAAATGAAGGACCCTT 58.491 40.909 0.04 0.04 39.23 3.95
4427 11364 3.903090 TGATGCAAAATGAAGGACCCTTT 59.097 39.130 2.43 0.00 36.26 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 1.920574 CGACTTGTAGTTGGCGATGAG 59.079 52.381 0.00 0.00 0.00 2.90
138 144 5.363562 TGCTTGATGACTTGATGTCCTAT 57.636 39.130 0.00 0.00 44.75 2.57
139 145 4.824479 TGCTTGATGACTTGATGTCCTA 57.176 40.909 0.00 0.00 44.75 2.94
140 146 3.708403 TGCTTGATGACTTGATGTCCT 57.292 42.857 0.00 0.00 44.75 3.85
141 147 3.066342 CCATGCTTGATGACTTGATGTCC 59.934 47.826 0.22 0.00 44.75 4.02
189 214 0.235665 CACAGATCAACGCAAACGCT 59.764 50.000 0.00 0.00 45.53 5.07
195 220 3.812609 ACAAATACACACAGATCAACGCA 59.187 39.130 0.00 0.00 0.00 5.24
210 235 3.930848 CACCTCGAACCCTACACAAATAC 59.069 47.826 0.00 0.00 0.00 1.89
212 237 2.290071 CCACCTCGAACCCTACACAAAT 60.290 50.000 0.00 0.00 0.00 2.32
213 238 1.071071 CCACCTCGAACCCTACACAAA 59.929 52.381 0.00 0.00 0.00 2.83
214 239 0.682852 CCACCTCGAACCCTACACAA 59.317 55.000 0.00 0.00 0.00 3.33
340 365 4.814294 GCGTCGCTGGGGTGGTAG 62.814 72.222 10.68 0.00 0.00 3.18
403 428 1.681793 ACGTTGACAGGGGAGATATCG 59.318 52.381 0.00 0.00 0.00 2.92
470 495 5.825679 ACAGCCTCTGAGATACAGTAAGTAG 59.174 44.000 6.17 0.00 45.86 2.57
472 497 4.605183 ACAGCCTCTGAGATACAGTAAGT 58.395 43.478 6.17 0.00 45.86 2.24
499 537 1.739067 CGGGAAATCACAGAGGGAAC 58.261 55.000 0.00 0.00 0.00 3.62
500 538 0.035439 GCGGGAAATCACAGAGGGAA 60.035 55.000 0.00 0.00 0.00 3.97
501 539 1.602237 GCGGGAAATCACAGAGGGA 59.398 57.895 0.00 0.00 0.00 4.20
504 542 0.807667 CTCCGCGGGAAATCACAGAG 60.808 60.000 27.83 7.08 0.00 3.35
507 545 1.375396 CACTCCGCGGGAAATCACA 60.375 57.895 27.83 1.15 0.00 3.58
512 550 3.234630 CTGGACACTCCGCGGGAAA 62.235 63.158 27.83 4.76 40.17 3.13
520 558 2.146920 AGTACCTAGCTGGACACTCC 57.853 55.000 0.00 0.00 39.71 3.85
529 567 5.513267 CCAAGAACTTCCAAAGTACCTAGCT 60.513 44.000 0.00 0.00 41.91 3.32
530 568 4.695928 CCAAGAACTTCCAAAGTACCTAGC 59.304 45.833 0.00 0.00 41.91 3.42
531 569 5.866207 ACCAAGAACTTCCAAAGTACCTAG 58.134 41.667 0.00 0.00 41.91 3.02
533 571 4.445879 GGACCAAGAACTTCCAAAGTACCT 60.446 45.833 0.00 0.00 41.91 3.08
534 572 3.819337 GGACCAAGAACTTCCAAAGTACC 59.181 47.826 0.00 0.00 41.91 3.34
535 573 4.715713 AGGACCAAGAACTTCCAAAGTAC 58.284 43.478 0.00 0.00 41.91 2.73
536 574 6.697641 ATAGGACCAAGAACTTCCAAAGTA 57.302 37.500 0.00 0.00 41.91 2.24
537 575 3.953542 AGGACCAAGAACTTCCAAAGT 57.046 42.857 0.00 0.00 45.46 2.66
538 576 6.265422 ACAAATAGGACCAAGAACTTCCAAAG 59.735 38.462 0.00 0.00 0.00 2.77
615 653 0.325203 AGCACCCCCGGCATATTTTT 60.325 50.000 0.00 0.00 0.00 1.94
616 654 0.325203 AAGCACCCCCGGCATATTTT 60.325 50.000 0.00 0.00 0.00 1.82
618 656 1.455587 CAAGCACCCCCGGCATATT 60.456 57.895 0.00 0.00 0.00 1.28
619 657 2.195683 CAAGCACCCCCGGCATAT 59.804 61.111 0.00 0.00 0.00 1.78
620 658 4.813235 GCAAGCACCCCCGGCATA 62.813 66.667 0.00 0.00 0.00 3.14
629 667 2.991540 GACCAAGGGGCAAGCACC 60.992 66.667 4.86 4.86 40.57 5.01
630 668 1.973812 GAGACCAAGGGGCAAGCAC 60.974 63.158 0.00 0.00 37.90 4.40
631 669 2.436109 GAGACCAAGGGGCAAGCA 59.564 61.111 0.00 0.00 37.90 3.91
632 670 2.747855 CGAGACCAAGGGGCAAGC 60.748 66.667 0.00 0.00 37.90 4.01
633 671 0.537371 AAACGAGACCAAGGGGCAAG 60.537 55.000 0.00 0.00 37.90 4.01
634 672 0.106419 AAAACGAGACCAAGGGGCAA 60.106 50.000 0.00 0.00 37.90 4.52
635 673 0.106419 AAAAACGAGACCAAGGGGCA 60.106 50.000 0.00 0.00 37.90 5.36
636 674 2.728397 AAAAACGAGACCAAGGGGC 58.272 52.632 0.00 0.00 37.90 5.80
719 757 3.066342 ACGTGATCGATTATCCGTTGAGT 59.934 43.478 0.00 0.00 37.89 3.41
725 763 0.702924 CGCACGTGATCGATTATCCG 59.297 55.000 22.23 5.02 40.62 4.18
738 776 2.860136 CAGATCACAATATGTCGCACGT 59.140 45.455 0.00 0.00 0.00 4.49
761 799 2.464189 CGAAACCGCACGTCTTCG 59.536 61.111 8.64 8.64 43.34 3.79
807 845 6.705825 ACAAAACAAAAAGAACTGCAGTTTCT 59.294 30.769 31.58 24.59 38.56 2.52
812 850 9.824534 AATAAAACAAAACAAAAAGAACTGCAG 57.175 25.926 13.48 13.48 0.00 4.41
836 874 8.611757 CAATTTTTCTTTCCCTCAAAACGAAAT 58.388 29.630 0.00 0.00 0.00 2.17
837 875 7.413548 GCAATTTTTCTTTCCCTCAAAACGAAA 60.414 33.333 0.00 0.00 0.00 3.46
838 876 6.036626 GCAATTTTTCTTTCCCTCAAAACGAA 59.963 34.615 0.00 0.00 0.00 3.85
839 877 5.522097 GCAATTTTTCTTTCCCTCAAAACGA 59.478 36.000 0.00 0.00 0.00 3.85
840 878 5.293079 TGCAATTTTTCTTTCCCTCAAAACG 59.707 36.000 0.00 0.00 0.00 3.60
901 939 8.680903 TGCTACTCCTATACAGTAGTACAAAAC 58.319 37.037 2.52 0.00 43.69 2.43
903 941 7.013083 GCTGCTACTCCTATACAGTAGTACAAA 59.987 40.741 2.52 0.00 43.69 2.83
904 942 6.485984 GCTGCTACTCCTATACAGTAGTACAA 59.514 42.308 2.52 0.00 43.69 2.41
905 943 5.996513 GCTGCTACTCCTATACAGTAGTACA 59.003 44.000 2.52 5.68 43.69 2.90
906 944 5.120519 CGCTGCTACTCCTATACAGTAGTAC 59.879 48.000 12.67 0.00 43.69 2.73
907 945 5.011431 TCGCTGCTACTCCTATACAGTAGTA 59.989 44.000 12.67 9.07 43.69 1.82
908 946 4.066490 CGCTGCTACTCCTATACAGTAGT 58.934 47.826 12.67 0.00 43.69 2.73
909 947 4.316645 TCGCTGCTACTCCTATACAGTAG 58.683 47.826 0.00 8.80 44.35 2.57
910 948 4.347360 TCGCTGCTACTCCTATACAGTA 57.653 45.455 0.00 0.00 0.00 2.74
911 949 3.210232 TCGCTGCTACTCCTATACAGT 57.790 47.619 0.00 0.00 0.00 3.55
912 950 4.291783 GTTTCGCTGCTACTCCTATACAG 58.708 47.826 0.00 0.00 0.00 2.74
913 951 3.067742 GGTTTCGCTGCTACTCCTATACA 59.932 47.826 0.00 0.00 0.00 2.29
914 952 3.067742 TGGTTTCGCTGCTACTCCTATAC 59.932 47.826 0.00 0.00 0.00 1.47
915 953 3.293337 TGGTTTCGCTGCTACTCCTATA 58.707 45.455 0.00 0.00 0.00 1.31
916 954 2.108168 TGGTTTCGCTGCTACTCCTAT 58.892 47.619 0.00 0.00 0.00 2.57
1019 1097 0.179059 TGCTGCACCGAACTGAAGAA 60.179 50.000 0.00 0.00 0.00 2.52
1041 5017 9.298774 GAAATACAGTACTACTCTAAATTGCGT 57.701 33.333 0.00 0.00 0.00 5.24
1058 5036 8.293699 ACCTTTTGACTTTTGAGAAATACAGT 57.706 30.769 0.00 0.00 0.00 3.55
1059 5037 7.587757 CGACCTTTTGACTTTTGAGAAATACAG 59.412 37.037 0.00 0.00 0.00 2.74
1060 5038 7.414436 CGACCTTTTGACTTTTGAGAAATACA 58.586 34.615 0.00 0.00 0.00 2.29
1061 5039 6.359883 GCGACCTTTTGACTTTTGAGAAATAC 59.640 38.462 0.00 0.00 0.00 1.89
1062 5040 6.262273 AGCGACCTTTTGACTTTTGAGAAATA 59.738 34.615 0.00 0.00 0.00 1.40
1063 5041 5.067805 AGCGACCTTTTGACTTTTGAGAAAT 59.932 36.000 0.00 0.00 0.00 2.17
1064 5042 4.398044 AGCGACCTTTTGACTTTTGAGAAA 59.602 37.500 0.00 0.00 0.00 2.52
1065 5043 3.945285 AGCGACCTTTTGACTTTTGAGAA 59.055 39.130 0.00 0.00 0.00 2.87
1674 5653 6.989659 AGTTTTGATTACCGTCTACTGAGAA 58.010 36.000 0.00 0.00 31.96 2.87
1675 5654 6.585695 AGTTTTGATTACCGTCTACTGAGA 57.414 37.500 0.00 0.00 0.00 3.27
1676 5655 6.033619 CGAAGTTTTGATTACCGTCTACTGAG 59.966 42.308 0.00 0.00 0.00 3.35
1677 5656 5.860182 CGAAGTTTTGATTACCGTCTACTGA 59.140 40.000 0.00 0.00 0.00 3.41
1692 5671 6.862090 AGCTCAACTAGTAGTACGAAGTTTTG 59.138 38.462 16.76 13.92 37.78 2.44
1779 5770 5.511729 GGAGTACAAAATATTTGCAGCGAAC 59.488 40.000 0.39 0.00 0.00 3.95
1782 5773 5.030295 CAGGAGTACAAAATATTTGCAGCG 58.970 41.667 0.39 0.00 0.00 5.18
1832 5824 3.838317 ACACTAGCAACTCCAATGTAGGA 59.162 43.478 0.00 0.00 36.00 2.94
1833 5825 4.207891 ACACTAGCAACTCCAATGTAGG 57.792 45.455 0.00 0.00 0.00 3.18
1834 5826 5.237815 TGAACACTAGCAACTCCAATGTAG 58.762 41.667 0.00 0.00 0.00 2.74
1835 5827 5.222079 TGAACACTAGCAACTCCAATGTA 57.778 39.130 0.00 0.00 0.00 2.29
1836 5828 4.085357 TGAACACTAGCAACTCCAATGT 57.915 40.909 0.00 0.00 0.00 2.71
1837 5829 4.275689 TGTTGAACACTAGCAACTCCAATG 59.724 41.667 10.89 0.00 43.52 2.82
1972 5964 4.096984 CCTACATCAGATTTGACAAAGGCC 59.903 45.833 6.77 0.00 35.83 5.19
1982 5974 9.136323 GAAATATCCCAAACCTACATCAGATTT 57.864 33.333 0.00 0.00 0.00 2.17
2297 6289 4.260620 GCCATGGATACGTAATTGTGTCAC 60.261 45.833 18.40 0.00 42.51 3.67
2434 6426 7.921786 TTTCCAGTGTACCAAATCAATCTAG 57.078 36.000 0.00 0.00 0.00 2.43
2483 6522 8.392372 ACCAAAGAGGATTTAAGACTGTAAAC 57.608 34.615 0.00 0.00 41.22 2.01
2546 6585 2.699251 CCAACAAGGGCTACGAAAAC 57.301 50.000 0.00 0.00 0.00 2.43
2609 6649 5.555017 AGGGTGCAATAGCTGAATACATAG 58.445 41.667 0.00 0.00 42.74 2.23
2775 6819 6.096705 CCCTTGATGCTATTTTGTATTGACCA 59.903 38.462 0.00 0.00 0.00 4.02
2784 6828 5.220854 CGGAAGTACCCTTGATGCTATTTTG 60.221 44.000 0.00 0.00 34.64 2.44
2785 6829 4.881850 CGGAAGTACCCTTGATGCTATTTT 59.118 41.667 0.00 0.00 34.64 1.82
2972 7163 6.127758 CGAACTGGATTGGTATCAATTTCCAA 60.128 38.462 11.35 0.00 43.08 3.53
2974 7165 5.588648 TCGAACTGGATTGGTATCAATTTCC 59.411 40.000 1.99 1.94 43.08 3.13
3061 7252 5.934625 GCCGAGTTCTTCATGACCATATATT 59.065 40.000 0.00 0.00 0.00 1.28
3555 7760 2.204136 TGCCATCCACCTCCCAGT 60.204 61.111 0.00 0.00 0.00 4.00
3627 7832 4.027572 TGGCAGTTTCTTCAGAAAAACG 57.972 40.909 3.51 0.00 44.58 3.60
3681 7886 5.761234 TGAACAATTTCGCTGGTAGTTTAGT 59.239 36.000 0.00 0.00 34.04 2.24
3687 7892 7.526608 TCTATTTTGAACAATTTCGCTGGTAG 58.473 34.615 0.00 0.00 34.04 3.18
3698 7903 6.077838 GCGAACGTTCTCTATTTTGAACAAT 58.922 36.000 24.80 0.00 41.67 2.71
3717 7922 2.514824 GCATCCCTCCTGGCGAAC 60.515 66.667 0.00 0.00 0.00 3.95
3756 7962 9.778993 AAAATGTCATACGAATCTGAAGAAATG 57.221 29.630 0.00 0.00 0.00 2.32
3825 8031 3.493503 GTGACGGTGACAGTTTTAGAAGG 59.506 47.826 0.00 0.00 0.00 3.46
3857 8070 4.976116 GCGACACATTTTCTTGCTAGTTTT 59.024 37.500 0.00 0.00 0.00 2.43
3930 8143 3.241995 GCCGTGTGATCTTTTAGCTAACG 60.242 47.826 5.45 3.75 0.00 3.18
3971 8184 6.718912 TGAAATGTGATGTCAATCCTTACCAA 59.281 34.615 0.00 0.00 31.15 3.67
3998 8211 3.425162 ACCCAAACAACCAAAGCAAAA 57.575 38.095 0.00 0.00 0.00 2.44
4053 8266 2.624838 CAAACCAAGCATAGGCCTATGG 59.375 50.000 40.67 32.27 42.32 2.74
4056 8269 1.919654 TCCAAACCAAGCATAGGCCTA 59.080 47.619 16.60 16.60 42.56 3.93
4077 8290 0.674895 CCTCCCGCAAGCTATATGGC 60.675 60.000 2.23 2.23 0.00 4.40
4138 8351 1.636519 TGGCTTCTTCCCGGGAATTAA 59.363 47.619 35.62 28.17 33.28 1.40
4191 8404 1.197721 CGAGTCCAAATGCACCACTTC 59.802 52.381 0.00 0.00 0.00 3.01
4282 11219 1.025113 GGGCCTAAAGCGTGAACTCC 61.025 60.000 0.84 0.00 45.17 3.85
4346 11283 2.172483 AACACGGGCTGCTCTAGTGG 62.172 60.000 11.40 0.00 37.16 4.00
4360 11297 1.604755 TCCAATTTTCACCGGAACACG 59.395 47.619 9.46 0.00 43.80 4.49
4361 11298 2.603652 CGTCCAATTTTCACCGGAACAC 60.604 50.000 9.46 0.00 31.35 3.32
4362 11299 1.604755 CGTCCAATTTTCACCGGAACA 59.395 47.619 9.46 0.00 31.35 3.18
4363 11300 1.068816 CCGTCCAATTTTCACCGGAAC 60.069 52.381 9.46 0.00 37.66 3.62
4364 11301 1.240256 CCGTCCAATTTTCACCGGAA 58.760 50.000 9.46 0.00 37.66 4.30
4365 11302 0.606944 CCCGTCCAATTTTCACCGGA 60.607 55.000 9.46 0.00 37.66 5.14
4366 11303 1.591504 CCCCGTCCAATTTTCACCGG 61.592 60.000 0.00 0.00 35.32 5.28
4367 11304 0.606944 TCCCCGTCCAATTTTCACCG 60.607 55.000 0.00 0.00 0.00 4.94
4368 11305 1.173913 CTCCCCGTCCAATTTTCACC 58.826 55.000 0.00 0.00 0.00 4.02
4369 11306 1.173913 CCTCCCCGTCCAATTTTCAC 58.826 55.000 0.00 0.00 0.00 3.18
4370 11307 0.610785 GCCTCCCCGTCCAATTTTCA 60.611 55.000 0.00 0.00 0.00 2.69
4371 11308 1.654023 CGCCTCCCCGTCCAATTTTC 61.654 60.000 0.00 0.00 0.00 2.29
4372 11309 1.677633 CGCCTCCCCGTCCAATTTT 60.678 57.895 0.00 0.00 0.00 1.82
4373 11310 2.045340 CGCCTCCCCGTCCAATTT 60.045 61.111 0.00 0.00 0.00 1.82
4374 11311 4.796495 GCGCCTCCCCGTCCAATT 62.796 66.667 0.00 0.00 0.00 2.32
4379 11316 4.899239 CTGATGCGCCTCCCCGTC 62.899 72.222 4.18 0.00 0.00 4.79
4381 11318 4.161295 TTCTGATGCGCCTCCCCG 62.161 66.667 4.18 0.00 0.00 5.73
4382 11319 2.514824 GTTCTGATGCGCCTCCCC 60.515 66.667 4.18 0.00 0.00 4.81
4383 11320 1.153086 ATGTTCTGATGCGCCTCCC 60.153 57.895 4.18 0.00 0.00 4.30
4384 11321 2.020131 CATGTTCTGATGCGCCTCC 58.980 57.895 4.18 0.00 0.00 4.30
4385 11322 1.354506 GCATGTTCTGATGCGCCTC 59.645 57.895 4.18 5.02 39.47 4.70
4386 11323 3.506108 GCATGTTCTGATGCGCCT 58.494 55.556 4.18 0.00 39.47 5.52
4402 11339 3.192466 GGTCCTTCATTTTGCATCATGC 58.808 45.455 1.35 1.35 45.29 4.06
4403 11340 3.449737 AGGGTCCTTCATTTTGCATCATG 59.550 43.478 0.00 0.00 0.00 3.07
4404 11341 3.716431 AGGGTCCTTCATTTTGCATCAT 58.284 40.909 0.00 0.00 0.00 2.45
4405 11342 3.173953 AGGGTCCTTCATTTTGCATCA 57.826 42.857 0.00 0.00 0.00 3.07
4406 11343 4.541973 AAAGGGTCCTTCATTTTGCATC 57.458 40.909 2.37 0.00 34.84 3.91


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.